Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / saezlab/liana-py issues and pull requests

#168 - LIANA+ in R

Issue - State: open - Opened by abadgerw 4 days ago - 1 comment

#167 - Installation issue on Google colab with GPU

Issue - State: open - Opened by wgao688 6 days ago - 2 comments
Labels: bug, help wanted

#166 - v1.5.1

Pull Request - State: closed - Opened by dbdimitrov 6 days ago

#164 - li.plotting.circle_plot error

Issue - State: open - Opened by gianfilippo 10 days ago - 2 comments

#163 - Inferred Network: multiple edges between same source-target pair

Issue - State: open - Opened by gianfilippo 11 days ago - 2 comments

#162 - blank plot from li.pl.tileplot and li.pl.dotplot

Issue - State: closed - Opened by gianfilippo 12 days ago - 1 comment

#161 - Fix dependencies and tests to support numpy>=2

Pull Request - State: closed - Opened by pablormier 13 days ago - 1 comment

#160 - AnnData version

Issue - State: closed - Opened by roshan9128 14 days ago - 3 comments
Labels: bug, help wanted

#159 - Visium HD bivariate output infer cell types?

Issue - State: open - Opened by RunyuXia 22 days ago - 1 comment

#158 - Circle Plot, interpretation

Issue - State: open - Opened by soniyalama 29 days ago - 1 comment

#157 - add Circle plot, address issues with AnnData, and scipy sparse

Pull Request - State: closed - Opened by dbdimitrov about 1 month ago

#156 - Mudata format for MOFA use.

Issue - State: closed - Opened by soniyalama about 1 month ago - 5 comments

#155 - Issues in bivariate.ipynb, likely related to package versions

Issue - State: closed - Opened by thomcsmits 2 months ago - 1 comment
Labels: bug, help wanted

#153 - Cell2cell or MOFA taking into account the spatial information

Issue - State: closed - Opened by kousaa 2 months ago - 2 comments
Labels: enhancement

#152 - Use of .obs features in bivariate statistics

Issue - State: closed - Opened by peterpdu 3 months ago - 6 comments
Labels: enhancement

#151 - Interpretation of negative PROGENY scores and context loadings

Issue - State: closed - Opened by wgao688 4 months ago - 1 comment
Labels: bug, help wanted

#150 - ImportError: cannot import name 'AlignedViewMixin'

Issue - State: closed - Opened by 1QiGuo 4 months ago - 4 comments
Labels: bug, help wanted

#149 - Is CORNETO installation incompatible with LIANA?

Issue - State: open - Opened by jiangzh-coder 4 months ago - 3 comments
Labels: bug, help wanted

#148 - module 'seaborn.categorical' has no attribute '_BoxPlotter'

Issue - State: closed - Opened by LJZYaaa 5 months ago - 1 comment

#147 - Obsm 'local_scores' needs to be of one specific type when running li.mt.bivariate

Issue - State: closed - Opened by dertrotl 5 months ago - 5 comments
Labels: bug, enhancement, help wanted

#146 - module 'liana.multi' has no attribute df_to_lr

Issue - State: closed - Opened by Elisa-blip 5 months ago - 1 comment
Labels: bug, help wanted

#145 - why the output dont include the cellchat part?

Issue - State: closed - Opened by LJZYaaa 5 months ago - 3 comments
Labels: bug, help wanted

#144 - Large number of pvals are `0` without specificity

Issue - State: closed - Opened by and-rewsmith 5 months ago - 4 comments
Labels: bug, help wanted

#143 - li.mt.bivariate: No common columns to perform merge on

Issue - State: open - Opened by rcannood 5 months ago - 1 comment
Labels: bug, help wanted

#142 - AttributeError: module 'corneto.methods.carnival' has no attribute '_extended_carnival_problem'

Issue - State: closed - Opened by gianfilippo 5 months ago - 7 comments
Labels: bug, help wanted

#141 - Option to aggregate individual MistyData objects from multiple samples

Issue - State: open - Opened by whitneyt1 5 months ago - 4 comments
Labels: enhancement

#140 - pin `anndata` to `<=0.10.8` due to scverse/mudata#77

Pull Request - State: closed - Opened by deeenes 6 months ago - 2 comments

#139 - circle_plot function for visualizing cell-cell communication

Pull Request - State: closed - Opened by WeipengMO 6 months ago - 3 comments

#138 - 1.4.0

Pull Request - State: closed - Opened by dbdimitrov 6 months ago

#137 - get_hcop_orthologs

Issue - State: open - Opened by tuhulab 6 months ago - 3 comments
Labels: bug, help wanted

#136 - Using data loader for performing tensor Factorization

Issue - State: closed - Opened by Mona1982 6 months ago - 9 comments
Labels: enhancement

#135 - CellChat AttributeError: 'SparseCSRView' object has no attribute 'A'

Issue - State: closed - Opened by AmyOlex 6 months ago - 5 comments
Labels: bug, help wanted

#134 - Support for Calligraphy ?

Issue - State: closed - Opened by divyanshusrivastava 6 months ago - 1 comment
Labels: enhancement

#133 - Guidelines to choose the best parameters for bivariate analysis using Visium HD data

Issue - State: open - Opened by Rafael-Silva-Oliveira 6 months ago - 5 comments
Labels: bug, help wanted

#132 - CCI network map for global LR interactions between cell types

Issue - State: closed - Opened by Rafael-Silva-Oliveira 6 months ago - 5 comments
Labels: enhancement

#131 - Does LIANA+ support Visium HD data?

Issue - State: closed - Opened by Rafael-Silva-Oliveira 7 months ago - 36 comments
Labels: enhancement

#130 - fail in running https://liana-py.readthedocs.io/en/latest/notebooks/misty.html

Issue - State: closed - Opened by huiyijiangling 7 months ago - 1 comment
Labels: bug, help wanted

#129 - Plot SVGs are massive in size due to color legend

Issue - State: closed - Opened by dnjst 7 months ago - 2 comments
Labels: bug, help wanted

#128 - Batch aware filtering of interactions in lrs_to_views

Issue - State: closed - Opened by robinfallegger 7 months ago - 4 comments
Labels: enhancement

#127 - Saving Misty model as .pkl

Issue - State: open - Opened by Zach-Sten 7 months ago - 3 comments
Labels: enhancement

#126 - Questions about LIANA+ requirement for cell number

Issue - State: open - Opened by jun-miao113 7 months ago - 3 comments
Labels: enhancement

#125 - v1.3.0

Pull Request - State: closed - Opened by dbdimitrov 7 months ago

#124 - Metabolite-protein interaction analysis did not show results

Issue - State: closed - Opened by cpy113 8 months ago - 5 comments
Labels: help wanted

#123 - Spatially informed bivariate metrics in tensor cell2cell and MOFA

Issue - State: closed - Opened by Zach-Sten 8 months ago - 3 comments
Labels: enhancement

#122 - Issue with orthologue conversion

Issue - State: closed - Opened by chrika2 8 months ago - 2 comments
Labels: bug, help wanted

#120 - pandas name index [BUG]

Issue - State: closed - Opened by dbdimitrov 8 months ago
Labels: bug, help wanted

#119 - v1.2.1

Pull Request - State: closed - Opened by dbdimitrov 8 months ago

#118 - Clarifications Differential analysis vignette

Issue - State: closed - Opened by maximelepetit 8 months ago - 1 comment
Labels: help wanted

#117 - Bug on Differential Expression Analysis for CCC & Downstream Signalling Networks Vignette

Issue - State: closed - Opened by maximelepetit 8 months ago - 3 comments
Labels: bug, help wanted

#116 - Import Error: Cannot Import name RandomForestModel

Issue - State: closed - Opened by poloarol 9 months ago - 3 comments
Labels: bug, help wanted

#115 - GeneA_GeneB gene expression level error

Issue - State: closed - Opened by alecdavi 9 months ago - 2 comments
Labels: bug, help wanted

#113 - Volcano plots for differentially expressed signaling pairs

Issue - State: closed - Opened by Zach-Sten 9 months ago - 2 comments
Labels: enhancement

#112 - Improve spatial neighbours function

Issue - State: closed - Opened by dbdimitrov 9 months ago
Labels: enhancement

#111 - Proper Caching for MetalinksDB & HCOP

Issue - State: open - Opened by dbdimitrov 9 months ago - 2 comments
Labels: enhancement

#110 - 1.2.0

Pull Request - State: closed - Opened by dbdimitrov 9 months ago

#109 - KeyError: None when using top_n parameter in li.pl.dotplot

Issue - State: closed - Opened by WeipengMO 9 months ago - 2 comments
Labels: bug, help wanted

#108 - Update _tileplot.py for plotnine >=0.13

Pull Request - State: closed - Opened by redst4r 9 months ago - 1 comment

#107 - LR_means, meaning?

Issue - State: closed - Opened by soniyalama 9 months ago - 2 comments

#106 - bandwith in multiple samples

Issue - State: closed - Opened by SopjudeS 10 months ago - 4 comments
Labels: bug, help wanted

#104 - Sanity check if liana uses the log normalised values

Issue - State: open - Opened by ahmetrifaioglu 10 months ago - 1 comment
Labels: enhancement

#103 - AnnData dtype argument deprecation

Issue - State: open - Opened by dbdimitrov 10 months ago
Labels: enhancement

#102 - Clarify LIANA + MOFA vignette

Issue - State: closed - Opened by dbdimitrov 10 months ago - 2 comments
Labels: enhancement

#101 - MOFA talk with multiple samples

Issue - State: closed - Opened by nicolebussola 10 months ago - 1 comment
Labels: bug, help wanted

#100 - Add a tutorial on GPU-accelerated misty

Issue - State: open - Opened by dbdimitrov 10 months ago
Labels: enhancement

#99 - Export Elbow plot from nmf

Issue - State: open - Opened by dbdimitrov 10 months ago
Labels: enhancement

#98 - v1.1.0

Pull Request - State: closed - Opened by dbdimitrov 10 months ago

#97 - ValueError: Please check if appropriate organism/ID type was provided!

Issue - State: closed - Opened by anke-king 11 months ago - 6 comments
Labels: bug, help wanted

#96 - Liana on pseduo bulk-sc data data

Issue - State: closed - Opened by Marwansha 11 months ago - 6 comments
Labels: help wanted

#95 - code li.pl.dotplot output an disappointing result

Issue - State: closed - Opened by Fanyu000 11 months ago - 5 comments

#94 - Flow chart to guide standard LIANA+ workflows

Issue - State: closed - Opened by dbdimitrov 11 months ago
Labels: enhancement

#93 - ZeroDivisionError: float division by zero

Issue - State: open - Opened by anke-king 11 months ago - 10 comments
Labels: help wanted

#92 - Add a check that for the subset of cell types in `li.multi.dea_to_lr`

Issue - State: closed - Opened by dbdimitrov 11 months ago
Labels: enhancement

#91 - v1.0.5

Pull Request - State: closed - Opened by dbdimitrov 12 months ago

#90 - Move Vignettes to Another Repo

Issue - State: open - Opened by dbdimitrov 12 months ago
Labels: documentation, enhancement

#89 - Magnitude ranks identical in same sample across cell type

Issue - State: closed - Opened by ShadHOH about 1 year ago - 2 comments
Labels: bug, help wanted

#88 - Question regarding ranking and aggregating from all methods.

Issue - State: closed - Opened by Marwansha about 1 year ago - 5 comments
Labels: help wanted

#87 - Error with li.mt.rank_aggregate.by_sample

Issue - State: closed - Opened by Marwansha about 1 year ago - 2 comments
Labels: bug, help wanted

#86 - Update MOFAcell Tutorial

Issue - State: closed - Opened by dbdimitrov about 1 year ago
Labels: enhancement

#85 - Frequency Chord diagram and Heatmap in Python

Issue - State: open - Opened by maximelepetit about 1 year ago - 10 comments
Labels: enhancement

#84 - Getting an error in liana multi df_to_lr

Issue - State: closed - Opened by ndrubins about 1 year ago - 15 comments
Labels: bug, help wanted

#83 - move LIANA+ plots to matplotlib and seaborn? [User Opinons Welcome]

Issue - State: open - Opened by dbdimitrov about 1 year ago
Labels: enhancement

#82 - Generate Union of Causal Net Predictions

Issue - State: closed - Opened by dbdimitrov about 1 year ago
Labels: enhancement

#81 - Difference on dotplot when running Steady-state Ligand-Receptor inference vignette from the Rank Aggregate section

Issue - State: closed - Opened by maximelepetit about 1 year ago - 3 comments
Labels: bug, help wanted

#80 - Error in function documentation / vignette

Issue - State: closed - Opened by maximelepetit about 1 year ago - 2 comments

#79 - v1.0.4

Pull Request - State: closed - Opened by dbdimitrov about 1 year ago

#78 - Implement GPU to speed up the CCC caculation in process of rank_aggregate method (CellChat part)?

Issue - State: open - Opened by xflicsu about 1 year ago - 1 comment
Labels: enhancement

#77 - Trouble with liana: 'liana.resource' has no attribute 'explode_complexes'

Issue - State: closed - Opened by merlevede about 1 year ago - 4 comments
Labels: question

#76 - The mouse resource are missing important interactions that should be possible to convert

Issue - State: closed - Opened by johan-gson about 1 year ago - 4 comments
Labels: bug, help wanted

#75 - Should we exclude CellTalkDB from curated resources list?

Issue - State: open - Opened by dbdimitrov about 1 year ago - 4 comments
Labels: enhancement, question

#74 - External + GPU-enabled MISTy models

Issue - State: closed - Opened by dbdimitrov over 1 year ago

#73 - Add bumpversion + metadata

Issue - State: closed - Opened by dbdimitrov over 1 year ago
Labels: enhancement

#72 - update env and version

Pull Request - State: closed - Opened by dbdimitrov over 1 year ago

#71 - ValueError: Observations annot. `var` must have as many rows as `X` has columns...

Issue - State: closed - Opened by mj-jimenez over 1 year ago - 3 comments
Labels: bug, help wanted

#70 - Additional metadata in results dataframe

Issue - State: open - Opened by dnjst over 1 year ago - 2 comments
Labels: enhancement

#69 - v1.0.3

Pull Request - State: closed - Opened by dbdimitrov over 1 year ago